Gamasutra has published a postmortem for the hugely successful Bioshock; nothing contained within is particularly shocking (though comments have groused that they left out some big snafus), though I think it's always interesting to see what participants in the creation process have to say about the success (or lack thereof). The article goes beyond game elements and gets into things like how design teams were organized. But where does Alyssa Finley, project lead, have to say about the problems the Bioshock team ran into?:

Our goal when we set out to make BioShock was very clear. We wanted to get to the next level, moving beyond our suite of critically acclaimed games to make a blockbuster. A lot of factors aligned to make this possible: the commercial backing of 2K; the game design knowledge we'd acquired from building System Shock 2; the technological familiarity with our Unreal-based engine that we'd built with previous games. But we still had to figure out how to make it all big-blockbuster big. A lot of our problems came from underestimating how big the task of making a triple-A product for multiple platforms and multiple regions really is. And other problems came from over-estimating our capacity to solve those problems using our existing procedures and staffing levels. If there's an over-arching theme of our development, it's that we, like many other developers, believe that ultimate success in this industry comes from iteration. You have to build, evaluate (and have others evaluate) and be prepared to throw things away and rebuild.